unallocated cheque balance

I have allocated a payment to account for one of our suppliers so that I could reconcile bank and come back to match account when time available. The supplier has paid us for two invoices previously paid and has not settled some invoices in full. When I try to match the bona fida invoices and part payments to payment to account I get the unallocated cheque message. All I want is to settle correct invoices and leave the unallocated payments as payments to account for future matching